Programme Monday 4 November 2019 11:00 - 13:00 Arrival / Registration with light refreshments Pre-conference workshop hosted by Samplix at 11:30-12:30 in Helix Seminar Room A 13:00 - 13:15 Opening remarks ATC Auditorium 13:15 - 16:30 Session 1: Cancer genetics and mutation ATC Auditorium 13:15 - 13:45 Somatic evolution in healthy and diseased bladder 1 urothelium Inigo Martincorena Wellcome Trust Sanger Institute, United Kingdom 13:45 - 14:00 A pan-cancer analysis reveals nonstop mutations causing 2 SMAD4 tumor suppressor degradation Sven Diederichs University of Freiburg, Germany 14:00 - 14:15 Large-scale analysis of liver cancer evolution in five 3 species Duncan Odom German Cancer Research Center (DKFZ), Germany 14:15 - 14:45 Full-length transcript isoforms associated with SF3B1 4 mutation in chronic lymphocytic leukemia Angela Brooks University of California, Santa Cruz, United States of America 14:45 - 15:15 Coffee break ATC Auditorium Foyer 15:15 - 15:45 Understanding epitopes that drive T cell activation 5 in cancer Matthew L. Meyerson Dana-Farber Cancer Institute, United States of America Page 5 EMBL Conference: Cancer Genomics 15:45 - 16:00 Comparison of somatic mutational processes across 6 mammalian species Alex Cagan Wellcome Trust Sanger Institute, United Kingdom 16:00 - 16:15 Genotoxic pks+ E. coli induces a unique mutational 7 signature in human colorectal cancer Axel Rosendahl Huber Princess Máxima Center, The Netherlands 16:15 - 16:30 Oxidative DNA damage repair switches mutagenic 8 outcomes in coding sequence dependent on the epigenome Anna Poetsch St. Anna Children's Cancer Research Institute, Austria 16:30 - 17:00 Coffee break ATC Auditorium Foyer 17:00 - 18:00 Keynote: Hereditary predisposition to childhood cancer 9 Stefan M. Pfister Hopp Children's Cancer Center Heidelberg (KiTZ), Germany 18:00 - 18:45 Digital poster presentations & Meet the speakers of Day 1 ATC Auditorium Foyer 18:45 - 20:15 Dinner EMBL Canteen 20:15 - 22:00 After-dinner drinks ATC Rooftop Lounge Page 6 Programme Tuesday 5 November 2019 09:00 - 12:15 Session 2: Cancer & microenvironment: immunogenomics & single cells ATC Auditorium 09:00 - 09:30 Building personalized cancer vaccines 10 Catherine J. Wu Dana-Farber Cancer Institute and Harvard Medical School, United States of America 09:30 - 09:45 Single-cell transcriptomics predicts relapse in infants with 11 acute lymphoblastic leukemia Frank Holstege Princess Máxima Center for Pediatric Oncology, The Netherlands 09:45 - 10:00 Computational study of the mechanisms of response to 12 immunotherapy by transcriptomic analysis of the tumor immune microenvironment in melanoma Yamil Damian Mahmoud Instituto de Biología y Medicina Experimental – CONICET, Argentina 10:00 - 10:30 Tumor genomic profiling to identify therapeutic biomarkers 13 and guide clinical care Michael F. Berger Memorial Sloan Kettering Cancer Center, United States of America 10:30 - 11:00 Coffee break ATC Auditorium Foyer 11:00 - 11:30 Somatic mutations in normal tissues 14 Peter Campbell Wellcome Trust Sanger Institute, United Kingdom Page 7 EMBL Conference: Cancer Genomics 11:30 - 11:45 Complex genomic rearrangements induced by ionizing 15 radiation in normal cells Jeonghwan Youk Korea Advanced Institute of Science and Technology, Republic of Korea 11:45 - 12:00 Lack of HLA affinity-based neoantigen depletion signals in 16 the cancer genome when considering mutational sequence contexts Jimmy Van den Eynden Ghent University, Belgium 12:00 - 12:15 Life history of normal human lymphocytes revealed by 17 somatic mutations Heather Machado Wellcome Trust Sanger Institute, United Kingdom 12:15 - 13:45 Lunch ATC Auditorium Foyer 13:45 - 15:15 Poster Session 1 (odd numbers) ATC Helix A 15:15 - 18:00 Session 3: Cancer genome and epigenome ATC Auditorium 15:15 - 15:45 Deciphering the evolutionary paths of tumor progression in 18 Small Cell Lung Cancer Julie George University of Cologne, Germany 15:45 - 16:00 Epigenetic and transcriptional reprogramming underlies 19 lung adenocarcinoma histological intra-tumor heterogeneity and microenvironment composition Giovanni Ciriello University of Lausanne, Switzerland Page 8 Programme 16:00 - 16:15 Reconstructing shattered chromosomes in oesophageal 20 adenocarcinomas Jannat Ijaz Wellcome Trust Sanger Institute, United Kingdom 16:15 - 16:45 Genomic alterations across molecular subtypes of mantle 21 cell lymphoma Elías Campo Hospital Clinic of the University of Barcelona, IDIBAPS, Spain 16:45 - 17:15 Coffee break & Meet the speakers of Day 2 ATC Auditorium Foyer 17:15 - 17:30 Aberrant integration of Hepatitis B virus DNA promotes 22 restructuring of hepatocellular carcinoma genome Eva Alvarez CIMUS, University of Santiago de Compostela, Spain 17:30 - 18:00 To be presented on-site 23 Sean Grimmond University of Melbourne, Australia 18:00 - 19:00 Partnering with patients to accelerate cancer genomics 24 and precision medicine Nikhil Wagle Dana-Farber Cancer Institute, United States of America 19:00 - 19:15 Apéritif ATC Auditorium Foyer 19:15 - 21:15 Conference Dinner EMBL Canteen 21:15 - 00:00 Conference Party with DJ ATC Auditorium Foyer Page 9 EMBL Conference: Cancer Genomics Wednesday 6 November 2019 09:00 - 12:00 Session 4: Drivers of cancer and genome-wide functional screens ATC Auditorium 09:00 - 09:30 Accelerating prediction of tumor vulnerabilities using 25 precision functional genomics Jesse S. Boehm Broad Institute, United States of America 09:30 - 09:45 The U1 spliceosomal RNA is recurrently mutated in 26 multiple cancers Shimin Shuai Ontario Institute for Cancer Research, Canada 09:45 - 10:00 Functional genomic studies of cancer immune evasion 27 using in vitro and in vivo CRISPR/Cas9 genetic screens Dimitrios Garyfallos University of Cambridge, United Kingdom 10:00 - 10:30 The mutational footprints of cancer therapies 28 Nuria Lopez-Bigas Institute for Research in Biomedicine (IRB Barcelona), Spain 10:30 - 11:00 Coffee break ATC Auditorium Foyer 11:00 - 11:30 To be presented on-site 29 Jan Korbel EMBL Heidelberg, Germany 11:30 - 11:45 Uncovering the role of the disruption of ubiquitin mediated 30 proteolysis in tumorigenesis Francisco Martinez-Jimenez Institute for Research in Biomedicine (IRB Barcelona), Spain Page 10 Programme 11:45 - 12:00 Elevated pyrimidine dimer formation at distinct genomic 31 bases underlies promoter mutation hotspots in UV-exposed cancers Kerryn Elliott University of Gothenburg, Sweden 12:00 - 13:30 Lunch & Meet the speakers of Day 3 (13:00-13:30) ATC Auditorium Foyer 13:30 - 15:00 Poster session 2 (even numbers) ATC Helix A 15:00 - 17:00 Session 5: Cancer genome medicine ATC Auditorium 15:00 - 15:30 To be presented on-site 32 Mathew Garnett Wellcome Trust Sanger Institute, United Kingdom 15:30 - 15:45 The evolutionary dynamics and fitness landscape of clonal 33 haematopoiesis Jamie Blundell University of Cambridge, United Kingdom 15:45 - 16:00 CRUK Grand Challenge Mutographs: Mutation signature 34 analysis of Oesophageal Squamous Cell Carcinoma (ESCC) from high incidence regions Sarah Moody Wellcome Trust Sanger Institute, United Kingdom 16:00 - 16:30 Oncologic therapy shapes the fitness landscape of clonal 35 hematopoiesis Elli Papaemmanuil Memorial Sloan Kettering Cancer Center, United States of America 16:30 - 17:00 Ngs-based molecular minimal residual disease detection 36 in acute myeloid leukemia Peter J.M. Valk Erasmus University Medical Center, The Netherlands Page 11 EMBL Conference: Cancer Genomics 17:00 - 17:15 Closing remarks and poster prize ATC Auditorium 17:30 Bus departures downtown and to Frankfurt Airport (Airport shuttle tickets for sale at registration desk) ATC Bus stop Page 12 .